ABSTRACT
The macroscopic single-celled green alga Acetabularia acetabulum has been a model system in cell biology for more than a century. However, no genomic information is available from this species. Since the alga has a long life cycle, is difficult to grow in dense cultures, and has an estimated diploid genome size of almost 2 Gb, obtaining sufficient genomic material for genome sequencing is challenging. Here, we have attempted to overcome these challenges by amplifying genomic DNA using multiple displacement amplification (MDA) combined with microfluidics technology to distribute the amplification reactions across thousands of microscopic droplets. By amplifying and sequencing DNA from five single cells we were able to recover an estimated ~ 7-11% of the total genome, providing the first draft of the A. acetabulum genome. We highlight challenges associated with genome recovery and assembly of MDA data due to biases arising during genome amplification, and hope that our study can serve as a reference for future attempts on sequencing the genome from non-model eukaryotes.
Subject(s)
Acetabularia/genetics , Nucleic Acid Amplification Techniques/methods , Whole Genome Sequencing , Acetabularia/cytology , Acetabularia/isolation & purification , DNA/genetics , Genome , Molecular Sequence Annotation , RNA, Messenger/genetics , RNA, Messenger/metabolism , Transcription, GeneticABSTRACT
Protoplasts were isolated from cells of Acetabularia cliftonii, which are presumed to be haploid. The release of the protoplasts occurred after treatment of the cells with papain or proteinase K. They are genuine protoplasts since they contain a nucleus. Fusion was initiated by mechanically pushing together two protoplasts. Under these conditions, the efficiency of fusion was more than 90% within 30 minutes at room temperature. Haploid cells from one cyst, i.e., cells which eventually would have formed gametes of the same mating type, exhibit a greater propensity for fusion as compared to haploid cells from different cysts.
